Question: Duplicates in plink files (same position, same ref allele but different A1 allele)
0
gravatar for Mamta
3.9 years ago by
Mamta450
United States
Mamta450 wrote:

HI all,

I remove duplicate snaps from my files using --list-duplicate vars. However this does not remove the snps with same position , same ref allele but different A1 - one has 0 ).

This creates problem when running shapeit, how do I remove these snaps?

Thanks, mamta

snpchip plink gwas • 1.6k views
ADD COMMENTlink modified 14 months ago by Hasanga0 • written 3.9 years ago by Mamta450

Hi,

I have the same problem as you. Did you manage to find a solution? You'll be kind to share with me if you have.

Thanks !

ADD REPLYlink modified 14 months ago • written 14 months ago by Hasanga0

Do the SNPs come from normalized VCF, in which multiple alternative alleles have been split into multiple SNP entires? If so, you may be able to fix it by choosing only one alternative allele in VCF then pipe it into plink.

ADD REPLYlink written 14 months ago by Vitis2.3k
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